CHECKPOINT_INFILE = "chkpts1"
CHECKPOINT_OUTFILE = "chkpts1"
CHECKPOINT_ITERATIONS = 50
ITERATIONS = 2000000
TIME_STEP = 2e-7
VACANCY_SEARCH_DISTANCE = 10

INCLUDE_FILE = "Scene.initialization.mdl"

PARTITION_X = [[-0.150999993085861 TO 0.150999993085861 STEP 0.0199999995529652]]
PARTITION_Y = [[-0.150999993085861 TO 0.150999993085861 STEP 0.0199999995529652]]
PARTITION_Z = [[-0.865317583084106 TO 0.0124999992549419 STEP 0.0199999995529652]]

INCLUDE_FILE = "Scene.molecules.mdl"

INCLUDE_FILE = "Scene.surface_classes.mdl"

INCLUDE_FILE = "Scene.reactions.mdl"

INCLUDE_FILE = "Scene.geo2d.mdl"

INCLUDE_FILE = "Scene.mod_surf_regions.mdl"

INSTANTIATE Scene OBJECT
{
  cleft OBJECT cleft {}
  glut_det1 OBJECT glut_det1 {}
  glut_det2 OBJECT glut_det2 {}
  postsynaptic OBJECT postsynaptic {}
  presynaptic OBJECT presynaptic {}
  Glut_release RELEASE_SITE
  {
   SHAPE = SPHERICAL
   LOCATION = [0.05, -0.05, 0]
   SITE_DIAMETER = 0.005
   MOLECULE = glutamate
   NUMBER_TO_RELEASE = 1500
   RELEASE_PROBABILITY = 1
  }
  uptake_site RELEASE_SITE
  {
   SHAPE = Scene.presynaptic[uptake_region]
   MOLECULE = EEAT,
   NUMBER_TO_RELEASE = 1000
   RELEASE_PROBABILITY = 1
  }
  AMPAR_release_cluster RELEASE_SITE
  {
   SHAPE = Scene.postsynaptic[release_cluster]
   MOLECULE = AMPAR'
   NUMBER_TO_RELEASE = 20
   RELEASE_PROBABILITY = 1
  }
  NMDAR_release_cluster RELEASE_SITE
  {
   SHAPE = Scene.postsynaptic[release_cluster]
   MOLECULE = NMDAR'
   NUMBER_TO_RELEASE = 20
   RELEASE_PROBABILITY = 1
  }
  AMPA_non_release_cluster RELEASE_SITE
  {
   SHAPE = Scene.postsynaptic[non_release_cluster]
   MOLECULE = AMPAR'
   NUMBER_TO_RELEASE = 20
   RELEASE_PROBABILITY = 1
  }
  NMDAR_non_release_cluster RELEASE_SITE
  {
   SHAPE = Scene.postsynaptic[non_release_cluster]
   MOLECULE = NMDAR'
   NUMBER_TO_RELEASE = 20
   RELEASE_PROBABILITY = 1
  }
}

sprintf(seed,"%05g",SEED)

INCLUDE_FILE = "Scene.viz_output.mdl"

INCLUDE_FILE = "Scene.rxn_output.mdl"